Pvt1 silencing in C2C12 cell cultures
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA449371 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to understand the role of lncRNA Pvt1 in skeletal muscle physiopathology we silenced this transcript in-vitro, using C2C12 cell cultures, and in-vivo, in leg muscles of CD1 wild-type and denervated mice.
2019-01-07 | GSE112881 | GEO
Project description:Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function it is fundamental to determine their expression in single cells, to identify their subcellular localization and eventually DNA interacting regions. In fact, lncRNAs present a cell-type specific expression and different functions depending on their subcellular localization. C2C12 cells are a model to study muscle pathophysiology and differentiation. We used this model to evaluate Pvt1-DNA interacting regions. We demonstrated that the lncRNA Pvt1, early activated during muscle atrophy, regulate the transcription of DNA and influence mitochondrial respiration and morphology ultimately impinging mito/autophagy and myofiber size in vivo. We evidenced that the long non-coding RNA Pvt1 is highly expressed during skeletal muscle atrophy. Moreover, it is preferentially expressed in fast contracting myofibers. By using high throughput techniques and Fluorescent In Situ Hybridization we evidenced that Pvt1 localize inside the nucleai of myofibers and C2C12 cells. C2C12 cells are widely used as in vitro model to study different aspects of muscle biology such as development, differentiation and metabolism. Because Pvt1 nuclear localization we checked its capacity to interact with DNA by Chromatin isolation by RNA purification (ChIRP).
2020-04-29 | GSE112977 | GEO
Project description:lncRNA PVT1 is an emerging lncRNA of significance in cancer due to alterations in both the RNA and genomic locus in multiple cancers and its established relationship to the oncogene MYC. Several recent studies have documented potential important roles for the lncRNA in ovarian cancer. Herein RNA sequencing was performed to determine the impact of PVT1 on global gene expression by performing RNA sequencing in SK-OV3 cells after silencing PVT1 (siPVT1) of cells grown upon transient knockdown of the lncRNA PVT1. SK-OV3 cells were cultured to 50% confluence in 6 well plates. Pooled siRNA’s to human PVT1 or non targeting control siRNA’s from Dharmacon were used to transfect SK-OV3 cells for 48 hrs in full serum media carefully maintaining cell confluence to not exceed approximately 80%. This was followed by RNA extraction and verification of knockdown using primers to PVT1 followed by sequencing. We find that 450 protein coding genes were differentially expressed between control (siControl) and siPVT1 cells with 50 additional found to be non-protein coding. The top 50 differentially expressed genes include 12 that were downregulated by siPVT1 and 32 that were upregulated. Several pathways associated with metabolic and stress processes, ribosome biogenesis and ncRNA processing were altered based on GO pathway analysis. Additional pathways included pathways associated with cell motility and differentiation.
2022-07-06 | GSE185933 | GEO
Project description:Long intergenic non-coding RNA (lincRNA) PVT1 is an oncogene known to be overexpressed in various types of cancer. PVT1 high expression is associated with increased prostate cancer (PCa) risk while androgen-independent PCa progression is correlated with increased androgen receptor (AR) expression. However, the mechanism of PVT1 and AR involvement in the development of prostate cancer is still unclear. Here, we tested the hypothesis that PVT1 participates along with AR and the methyltransferase EZH2 from the Polycomb repressive complex 2 in the repression of gene expression in LNCaP prostate cancer cells. Native RNA-binding proteins immunoprecipitation followed by quantitative PCR of co-precipitated RNAs (RIP-qPCR) revealed that in LNCaP, PVT1 lincRNA is associated both with AR (10 – 12 % of PVT1 input) and EZH2 (36 – 42 % of input) in the presence or absence of androgen. PVT1 knockdown in LNCaP in the presence of androgen increased the expression of 160 genes whose expression was repressed by androgen, including genes involved in regulation of cell differentiation, in inhibition of cell migration/invasion and in triggering apoptosis. Analysis by chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) of the histone marks occupancy at the promoter region of the tumor suppressor gene NOV, one of the genes that had an increased expression upon PVT1 silencing, showed a significant epigenetic remodeling at its promoter and enhancer regions upon PVT1 knockdown. We provide evidence for a genome-wide transcriptional repressive role of PVT1 lincRNA on tumor suppressor genes in prostate cancer cells.
2021-01-19 | GSE133372 | GEO
Project description:Background Cutaneous squamous cell carcinoma (cSCC) is one of the most common and fastest increasing forms of cancer worldwide with metastatic potential. Long non-coding RNAs (lncRNAs) are a group of RNA-molecules with essential regulatory functions for both physiological and pathological processes. Objectives To investigate the function and mode of action of lncRNA plasmacytoma variant translocation 1 (PVT1) in cSCC. Methods The expression level of PVT1 was quantified in healthy skin, benign skin diseases and cSCCs by qRT-PCR and single molecule in situ hybridization. The function of PVT1 in cSCC was investigated both in vivo (tumour xenograft) and in vitro (competitive cell growth assay, EdU-incorporation assay, colony formation assay and tumour spheroid formation assay) by CRISPR-Cas9-mediated PVT1 or PVT1 exon 2 knockout and by locked nucleic acid (LNA) GapmeR-mediated PVT1-knockdown. RNAseq-analysis was conducted to identify genes and processes regulated by PVT1. Results We identified PVT1 as a lncRNA upregulated in cutaneous squamous cell carcinoma in situ (cSCCIS) and cSCC and associated with oncogenic phenotype of cSCC. The increased expression of PVT1 in cSCC was regulated by MYC. Both CRISPR-Cas9-deletion of the entire PVT1 locus and LNA GapmeR-mediated knockdown of PVT1-transcript impaired malignant behaviour of cSCC cells which suggested that PVT1 is an oncogenic transcript in cSCC. Furthermore, knockout of PVT1 exon 2 inhibited cSCC tumour growth both in vivo and in vitro demonstrating that exon 2 is a critical element for the oncogenic role of PVT1. Mechanistically, we show that PVT1 is localized in the cell nucleus and acts as a suppressor of cellular senescence by inhibiting CDKN1A expression and preventing cell cycle arrest. Conclusions Our study reveals a previously unrecognized role for exon 2 of PVT1 in its oncogenic role and that PVT1 suppresses cellular senescence. PVT1 may be a biomarker and therapeutic target in cSCC.
2023-11-30 | GSE235606 | GEO
Project description:Mus musculus strain:C2C12 cell Genome sequencing
| PRJDA72887 | ENA
Project description:Defining the function of TEAD transcription factors in myogenic differentiation has proved elusive due to overlapping expression and functional redundancy. Here, we show that siRNA silencing of either Tead1, Tead2 or Tead4 did not effect differentiation of primary myoblasts (PMs) while their simultaneous knockdown strongly impaired differentiation. In contrast in C2C12 cells, silencing of Tead1 or Tead4 impaired differentiation showing a differential requirement for these factors in PMs and C2C12 cells that involved both differential regulation of their expression and intracellular localisation. Through integration of Tead1 and Tead4 ChIP-seq with chromatin modifications, we identify active enhancers associated with genes activated during C2C12 cell differentiation that are bound by combinations of Tead4, Myod1 or Myog and show a signature of frequently co-occuring motifs. We show that distinct but overlapping sets of genes are deregulated by Tead silencing in C2C12 cells and PMs therefore describing for the first time in a comprehensive manner the specific and redundant regulatory roles of Tead factors in myogenic differentiation. We also performed ChIP-seq from mouse muscle in vivo identifying a set of highly transcribed muscle cell-identity genes and revealing that Tead4 binds a distinct repertoire of sites in C2C12 cells and muscle.
2017-02-17 | GSE82192 | GEO
Project description:Defining the function of TEAD transcription factors in myogenic differentiation has proved elusive due to overlapping expression and functional redundancy. Here, we show that siRNA silencing of either Tead1, Tead2 or Tead4 did not effect differentiation of primary myoblasts (PMs) while their simultaneous knockdown strongly impaired differentiation. In contrast in C2C12 cells, silencing of Tead1 or Tead4 impaired differentiation showing a differential requirement for these factors in PMs and C2C12 cells that involved both differential regulation of their expression and intracellular localisation. Through integration of Tead1 and Tead4 ChIP-seq with chromatin modifications, we identify active enhancers associated with genes activated during C2C12 cell differentiation that are bound by combinations of Tead4, Myod1 or Myog and show a signature of frequently co-occuring motifs. We show that distinct but overlapping sets of genes are deregulated by Tead silencing in C2C12 cells and PMs therefore describing for the first time in a comprehensive manner the specific and redundant regulatory roles of Tead factors in myogenic differentiation. We also performed ChIP-seq from mouse muscle in vivo identifying a set of highly transcribed muscle cell-identity genes and revealing that Tead4 binds a distinct repertoire of sites in C2C12 cells and muscle.
2017-02-17 | GSE82190 | GEO
Project description:We sought to determine the effects of over-expression of Gli1 on gene expression in C2C12 myotube cultures. C2C12 myoblasts were induced to differentiate for 4 days. At that time, when >80% of nuclei were incorporated into multi-nucleated syncitial myotubes, we infected the cultures with recombinant adenovirus expressing GFP alone or GFP and a full length human Gli1. Media was changed 12 hours later. Cultures were lysed 60 hours after the initial infection. Gli1 over-expression induces de-differentiation of myotubes and proliferation of myoblasts.
2013-12-01 | GSE37702 | GEO
Project description:We used RIP-seq to sequenceWT C2C12 and the C2C12 cell line overexpressing WT PrPc to investigate the miRNAs that PrPc in them specifically binds at the fourth day of C2C12 cell differentiation
2023-12-13 | GSE203419 | GEO